AndreaGuarracino
commented
1 month ago Have you already tried to merge the GFAs with odgi squeeze?
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From: Taek Wizard @.> Sent: Monday, September 9, 2024 8:36:00 PM To: vgteam/vg @.> Cc: Subscribed @.***> Subject: [vgteam/vg] Issue Converting PGGB GFA Files for Panacus (Issue #4392)
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What were you trying to do? Dear VG team, After generating GFA files for each chromosome using PGGB, I need to merge them for Panacus. However, the Panacus team confirmed that a simple cat command to merge PGGB GFA files won't work.
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What did you want to happen? I was advised to convert the PGGB GFA files into VG-compatible GFA format.
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What actually happened? Here’s what I tried in Step 2 (Convert PGGB GFA to VG-compatible GFA): vg convert -fW -t ${PBS_NCPUS} -g ${INPUT_GFA} > ${OUTPUT_DIR}/${BASEFILE}.vg1.gfa vg convert -f -t ${PBS_NCPUS} -g ${INPUT_GFA} > ${OUTPUT_DIR}/${BASEFILE}.vg2.gfa
Both commands produced only a single line: H VN:Z:1.1, without any error messages or meaningful output.
- If you got a line like Stack trace path: /somewhere/on/your/computer/stacktrace.txt, please copy-paste the contents of that file here:
Place stacktrace here.
- What data and command can the vg dev team use to make the problem happen?
The following steps would be: Step 3: Merge VG GFA files using vg combine vg combine $(find -L ${PGGB_GFA} -type f -name "*.vg.gfa") > ${OUTPUT_DIR}/chrAll_merged_pggb.smooth.final.vg.gfa
Step 4: Convert merged VG to GFA vg view --threads ${PBS_NCPUS} -F -v ${OUTPUT_DIR}/chrAll_merged_pggb.smooth.final.vg.gfa > ${OUTPUT_DIR}/chrAll_merged_pggb_convert.smooth.final.vg.gfa
Step 5: Validate final GFA file vg validate ${OUTPUT_DIR}/chrAll_merged_pggb_convert.smooth.final.vg.gfa
Unfortunately, Step 2 did not produce any usable output for proceeding with the next steps.
Do you have any suggestions on how to resolve this issue?
Regards,
Taek
- What does running vg version say?
No error messages or meaningful output.
I used vg version 1.56.0 from bioconda.
— Reply to this email directly, view it on GitHubhttps://github.com/vgteam/vg/issues/4392, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AO26XHXV6MLDFYJI6UOFBWLZVZSKBAVCNFSM6AAAAABN5Z6GNSVHI2DSMVQWIX3LMV43ASLTON2WKOZSGUYTKMZSGE4TONA. You are receiving this because you are subscribed to this thread.Message ID: @.***>
jeizenga
OZTaekOppa
1. What were you trying to do? Dear VG team, After generating GFA files for each chromosome using PGGB, I need to merge them for Panacus. However, the Panacus team confirmed that a simple cat command to merge PGGB GFA files won't work.
2. What did you want to happen? I was advised to convert the PGGB GFA files into VG-compatible GFA format.
3. What actually happened? Here’s what I tried in Step 2 (Convert PGGB GFA to VG-compatible GFA): vg convert -fW -t ${PBS_NCPUS} -g ${INPUT_GFA} > ${OUTPUT_DIR}/${BASEFILE}.vg1.gfa vg convert -f -t ${PBS_NCPUS} -g ${INPUT_GFA} > ${OUTPUT_DIR}/${BASEFILE}.vg2.gfa
Both commands produced only a single line: H VN:Z:1.1, without any error messages or meaningful output.
4. If you got a line like
Stack trace path: /somewhere/on/your/computer/stacktrace.txt, please copy-paste the contents of that file here:5. What data and command can the vg dev team use to make the problem happen?
The following steps would be: Step 3: Merge VG GFA files using vg combine vg combine $(find -L ${PGGB_GFA} -type f -name "*.vg.gfa") > ${OUTPUT_DIR}/chrAll_merged_pggb.smooth.final.vg.gfa
Step 4: Convert merged VG to GFA vg view --threads ${PBS_NCPUS} -F -v ${OUTPUT_DIR}/chrAll_merged_pggb.smooth.final.vg.gfa > ${OUTPUT_DIR}/chrAll_merged_pggb_convert.smooth.final.vg.gfa
Step 5: Validate final GFA file vg validate ${OUTPUT_DIR}/chrAll_merged_pggb_convert.smooth.final.vg.gfa
Unfortunately, Step 2 did not produce any usable output for proceeding with the next steps.
Do you have any suggestions on how to resolve this issue?
Regards,
Taek
6. What does running
vg versionsay?No error messages or meaningful output.